3TQ5

Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) COMPLEX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D4LPDB entry 2D4L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.141.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.714α = 90
b = 60.714β = 90
c = 63.775γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8128EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.42099.30.07113.42.72614826148-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4899.80.4172.62.24009

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONrigid body refinementTHROUGHOUTPDB entry 2D4L1.4202610824723138599.150.17970.1790.193RANDOM24.752
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.720.360.72-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.024
r_dihedral_angle_4_deg20.854
r_dihedral_angle_3_deg11.68
r_scangle_it6.193
r_dihedral_angle_1_deg5.999
r_scbond_it5.05
r_mcangle_it3.56
r_mcbond_it2.051
r_angle_refined_deg2.028
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.024
r_dihedral_angle_4_deg20.854
r_dihedral_angle_3_deg11.68
r_scangle_it6.193
r_dihedral_angle_1_deg5.999
r_scbond_it5.05
r_mcangle_it3.56
r_mcbond_it2.051
r_angle_refined_deg2.028
r_nbtor_refined0.324
r_symmetry_vdw_refined0.249
r_nbd_refined0.246
r_symmetry_hbond_refined0.235
r_xyhbond_nbd_refined0.223
r_chiral_restr0.14
r_bond_refined_d0.02
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms818
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing